PlotPhylochipHeatmap: PlotPhylochipHeatmap

In microbiome/HITChipDB: HITChipDB

Description

Plots heatmap of the oligo profiles together with phylotype grouping and sample clustering

Usage

PlotPhylochipHeatmap(
  data,
  taxonomy,
  metric = "pearson",
  level = "L1",
  tree.display = TRUE,
  palette = "white/black",
  fontsize = 40,
  figureratio = 10,
  hclust.method = "complete"
)

Arguments

data	oligoprofile data in original (non-log) domain
taxonomy	oligo-phylotype mappings
metric	clustering metric
level	taxonomic level to show (L0 / L1 / L2 / species)
tree.display	tree.display
palette	color palette ("white/black" / "white/blue" / "black/yellow/white")
fontsize	font size
figureratio	figure ratio
hclust.method	hierarchical clustering method. See help(hclust) for details. To prevent ordering of the rows, use hclust.method = NULL.

Value

parameters

Author(s)

Contact: Leo Lahti [e-mail]

References

See citation("microbiome")

Examples

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microbiome/HITChipDB documentation built on June 7, 2020, 8:25 a.m.